The Indian army was not deployed to deal with the gathering, and no such letter written by the army chiefs to Home Minister is publicly available.
The Indian Farm Reforms of 2020 refer to three agricultural bills passed by India's Parliament on Sep. 27, 2020. The Farmers' Produce Trade and Commerce, the Farmers Agreement of Price Assurance and Farm Services, and the Essential Commodities Act were passed by the House and received the President's assent turning them into laws.
On Sep. 24. 2020, farmers started a Rail Roko campaign, following which train services to and from Punjab were affected. On Oct. 23, some farmer unions decided to call off the drive, as supplies of fertilizer and other goods in the state were starting to run short. The Delhi march was accompanied by thousands of people across India on Nov. 27, 2020, in opposition to the farm law reforms. The farmers, mostly from Punjab and Haryana, had mobilized under the Samyukt Kisan Morcha banner for the Dilli Chalo agitation. The police had three layers of protection in place against the protestors. Huge cement blocks formed the first line of defense, followed by barricades with barbed wires and parked trucks, trailers, and small commercial vehicles forming the final security layer.
More than 100 veterans of the armed forces published a statement supporting farmers who are protesting against the three farm laws at Delhi's borders. "We stand in solidarity with the peacefully protesting farmers, empathize with them, and support their demands," the veterans have written. The veteran's brief statement also criticizes and condemns the police's tear gas and water cannon on farmers on Nov. 26 and 27. However, these veterans issued an open message to the Indian government.
There is no evidence to confirm whether Indian Defence chiefs have written a letter to Amit Shah that they can't chase away farmers' large gathering.
Moreover, the Indian army was not deployed to deal with the protest; the Delhi Police, which comes under the Union Home Ministry, was deployed to prevent the farmer's entry into the city. No other media outlets have reported on the contents of such a letter. Since there are no credible or official statements by the Indian Defence to verify the letter's authenticity, it is false.